.. _advanced-installation: .. include:: ../min_dependency_substitutions.rst ================================================== Installing the development version of scikit-learn ================================================== This section introduces how to install the **main branch** of scikit-learn. This can be done by either installing a nightly build or building from source. .. _install_nightly_builds: Installing nightly builds ========================= The continuous integration servers of the scikit-learn project build, test and upload wheel packages for the most recent Python version on a nightly basis. Installing a nightly build is the quickest way to: - try a new feature that will be shipped in the next release (that is, a feature from a pull-request that was recently merged to the main branch); - check whether a bug you encountered has been fixed since the last release. .. prompt:: bash $ pip install --pre --extra-index https://pypi.anaconda.org/scipy-wheels-nightly/simple scikit-learn .. _install_bleeding_edge: Building from source ==================== Building from source is required to work on a contribution (bug fix, new feature, code or documentation improvement). .. _git_repo: #. Use `Git `_ to check out the latest source from the `scikit-learn repository `_ on Github.: .. prompt:: bash $ git clone git://github.com/scikit-learn/scikit-learn.git # add --depth 1 if your connection is slow cd scikit-learn If you plan on submitting a pull-request, you should clone from your fork instead. #. Install a recent version of Python (3.9 is recommended at the time of writing) for instance using Miniforge3_. Miniforge provides a conda-based distribution of Python and the most popular scientific libraries. If you installed Python with conda, we recommend to create a dedicated `conda environment`_ with all the build dependencies of scikit-learn (namely NumPy_, SciPy_, and Cython_): .. prompt:: bash $ conda create -n sklearn-env -c conda-forge python=3.9 numpy scipy cython conda activate sklearn-env #. **Alternative to conda:** If you run Linux or similar, you can instead use your system's Python provided it is recent enough (3.7 or higher at the time of writing). In this case, we recommend to create a dedicated virtualenv_ and install the scikit-learn build dependencies with pip: .. prompt:: bash $ python3 -m venv sklearn-env source sklearn-env/bin/activate pip install wheel numpy scipy cython #. Install a compiler with OpenMP_ support for your platform. See instructions for :ref:`compiler_windows`, :ref:`compiler_macos`, :ref:`compiler_linux` and :ref:`compiler_freebsd`. #. Build the project with pip in :ref:`editable_mode`: .. prompt:: bash $ pip install --verbose --no-build-isolation --editable . #. Check that the installed scikit-learn has a version number ending with `.dev0`: .. prompt:: bash $ python -c "import sklearn; sklearn.show_versions()" #. Please refer to the :ref:`developers_guide` and :ref:`pytest_tips` to run the tests on the module of your choice. .. note:: You will have to run the ``pip install --no-build-isolation --editable .`` command every time the source code of a Cython file is updated (ending in `.pyx` or `.pxd`). Use the ``--no-build-isolation`` flag to avoid compiling the whole project each time, only the files you have modified. Dependencies ------------ Runtime dependencies ~~~~~~~~~~~~~~~~~~~~ Scikit-learn requires the following dependencies both at build time and at runtime: - Python (>= 3.7), - NumPy (>= |NumpyMinVersion|), - SciPy (>= |ScipyMinVersion|), - Joblib (>= |JoblibMinVersion|), - threadpoolctl (>= |ThreadpoolctlMinVersion|). .. note:: For running on PyPy, PyPy3-v5.10+, Numpy 1.14.0+, and scipy 1.1.0+ are required. For PyPy, only installation instructions with pip apply. Build dependencies ~~~~~~~~~~~~~~~~~~ Building Scikit-learn also requires: .. # The following places need to be in sync with regard to Cython version: # - .circleci config file # - sklearn/_build_utils/__init__.py # - advanced installation guide - Cython >= |CythonMinVersion| - A C/C++ compiler and a matching OpenMP_ runtime library. See the :ref:`platform system specific instructions ` for more details. .. note:: If OpenMP is not supported by the compiler, the build will be done with OpenMP functionalities disabled. This is not recommended since it will force some estimators to run in sequential mode instead of leveraging thread-based parallelism. Setting the ``SKLEARN_FAIL_NO_OPENMP`` environment variable (before cythonization) will force the build to fail if OpenMP is not supported. Since version 0.21, scikit-learn automatically detects and use the linear algebrea library used by SciPy **at runtime**. Scikit-learn has therefore no build dependency on BLAS/LAPACK implementations such as OpenBlas, Atlas, Blis or MKL. Test dependencies ~~~~~~~~~~~~~~~~~ Running tests requires: - pytest >= |PytestMinVersion| Some tests also require `pandas `_. Building a specific version from a tag -------------------------------------- If you want to build a stable version, you can ``git checkout `` to get the code for that particular version, or download an zip archive of the version from github. .. _editable_mode: Editable mode ------------- If you run the development version, it is cumbersome to reinstall the package each time you update the sources. Therefore it is recommended that you install in with the ``pip install --no-build-isolation --editable .`` command, which allows you to edit the code in-place. This builds the extension in place and creates a link to the development directory (see `the pip docs `_). This is fundamentally similar to using the command ``python setup.py develop`` (see `the setuptool docs `_). It is however preferred to use pip. On Unix-like systems, you can equivalently type ``make in`` from the top-level folder. Have a look at the ``Makefile`` for additional utilities. .. _platform_specific_instructions: Platform-specific instructions ============================== Here are instructions to install a working C/C++ compiler with OpenMP support to build scikit-learn Cython extensions for each supported platform. .. _compiler_windows: Windows ------- First, download the `Build Tools for Visual Studio 2019 installer `_. Run the downloaded `vs_buildtools.exe` file, during the installation you will need to make sure you select "Desktop development with C++", similarly to this screenshot: .. image:: ../images/visual-studio-build-tools-selection.png Secondly, find out if you are running 64-bit or 32-bit Python. The building command depends on the architecture of the Python interpreter. You can check the architecture by running the following in ``cmd`` or ``powershell`` console: .. prompt:: bash $ python -c "import struct; print(struct.calcsize('P') * 8)" For 64-bit Python, configure the build environment by running the following commands in ``cmd`` or an Anaconda Prompt (if you use Anaconda): :: $ SET DISTUTILS_USE_SDK=1 $ "C:\Program Files (x86)\Microsoft Visual Studio\2019\BuildTools\VC\Auxiliary\Build\vcvarsall.bat" x64 Replace ``x64`` by ``x86`` to build for 32-bit Python. Please be aware that the path above might be different from user to user. The aim is to point to the "vcvarsall.bat" file that will set the necessary environment variables in the current command prompt. Finally, build scikit-learn from this command prompt: .. prompt:: bash $ pip install --verbose --no-build-isolation --editable . .. _compiler_macos: macOS ----- The default C compiler on macOS, Apple clang (confusingly aliased as `/usr/bin/gcc`), does not directly support OpenMP. We present two alternatives to enable OpenMP support: - either install `conda-forge::compilers` with conda; - or install `libomp` with Homebrew to extend the default Apple clang compiler. For Apple Silicon M1 hardware, only the conda-forge method below is known to work at the time of writing (January 2021). You can install the `macos/arm64` distribution of conda using the `miniforge installer `_ macOS compilers from conda-forge ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ If you use the conda package manager (version >= 4.7), you can install the ``compilers`` meta-package from the conda-forge channel, which provides OpenMP-enabled C/C++ compilers based on the llvm toolchain. First install the macOS command line tools: .. prompt:: bash $ xcode-select --install It is recommended to use a dedicated `conda environment`_ to build scikit-learn from source: .. prompt:: bash $ conda create -n sklearn-dev -c conda-forge python numpy scipy cython \ joblib threadpoolctl pytest compilers llvm-openmp conda activate sklearn-dev make clean pip install --verbose --no-build-isolation --editable . .. note:: If you get any conflicting dependency error message, try commenting out any custom conda configuration in the ``$HOME/.condarc`` file. In particular the ``channel_priority: strict`` directive is known to cause problems for this setup. You can check that the custom compilers are properly installed from conda forge using the following command: .. prompt:: bash $ conda list which should include ``compilers`` and ``llvm-openmp``. The compilers meta-package will automatically set custom environment variables: .. prompt:: bash $ echo $CC echo $CXX echo $CFLAGS echo $CXXFLAGS echo $LDFLAGS They point to files and folders from your ``sklearn-dev`` conda environment (in particular in the bin/, include/ and lib/ subfolders). For instance ``-L/path/to/conda/envs/sklearn-dev/lib`` should appear in ``LDFLAGS``. In the log, you should see the compiled extension being built with the clang and clang++ compilers installed by conda with the ``-fopenmp`` command line flag. macOS compilers from Homebrew ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Another solution is to enable OpenMP support for the clang compiler shipped by default on macOS. First install the macOS command line tools: .. prompt:: bash $ xcode-select --install Install the Homebrew_ package manager for macOS. Install the LLVM OpenMP library: .. prompt:: bash $ brew install libomp Set the following environment variables: .. prompt:: bash $ export CC=/usr/bin/clang export CXX=/usr/bin/clang++ export CPPFLAGS="$CPPFLAGS -Xpreprocessor -fopenmp" export CFLAGS="$CFLAGS -I/usr/local/opt/libomp/include" export CXXFLAGS="$CXXFLAGS -I/usr/local/opt/libomp/include" export LDFLAGS="$LDFLAGS -Wl,-rpath,/usr/local/opt/libomp/lib -L/usr/local/opt/libomp/lib -lomp" Finally, build scikit-learn in verbose mode (to check for the presence of the ``-fopenmp`` flag in the compiler commands): .. prompt:: bash $ make clean pip install --verbose --no-build-isolation --editable . .. _compiler_linux: Linux ----- Linux compilers from the system ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Installing scikit-learn from source without using conda requires you to have installed the scikit-learn Python development headers and a working C/C++ compiler with OpenMP support (typically the GCC toolchain). Install build dependencies for Debian-based operating systems, e.g. Ubuntu: .. prompt:: bash $ sudo apt-get install build-essential python3-dev python3-pip then proceed as usual: .. prompt:: bash $ pip3 install cython pip3 install --verbose --editable . Cython and the pre-compiled wheels for the runtime dependencies (numpy, scipy and joblib) should automatically be installed in ``$HOME/.local/lib/pythonX.Y/site-packages``. Alternatively you can run the above commands from a virtualenv_ or a `conda environment`_ to get full isolation from the Python packages installed via the system packager. When using an isolated environment, ``pip3`` should be replaced by ``pip`` in the above commands. When precompiled wheels of the runtime dependencies are not available for your architecture (e.g. ARM), you can install the system versions: .. prompt:: bash $ sudo apt-get install cython3 python3-numpy python3-scipy On Red Hat and clones (e.g. CentOS), install the dependencies using: .. prompt:: bash $ sudo yum -y install gcc gcc-c++ python3-devel numpy scipy Linux compilers from conda-forge ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Alternatively, install a recent version of the GNU C Compiler toolchain (GCC) in the user folder using conda: .. prompt:: bash $ conda create -n sklearn-dev -c conda-forge python numpy scipy cython \ joblib threadpoolctl pytest compilers conda activate sklearn-dev pip install --verbose --no-build-isolation --editable . .. _compiler_freebsd: FreeBSD ------- The clang compiler included in FreeBSD 12.0 and 11.2 base systems does not include OpenMP support. You need to install the `openmp` library from packages (or ports): .. prompt:: bash $ sudo pkg install openmp This will install header files in ``/usr/local/include`` and libs in ``/usr/local/lib``. Since these directories are not searched by default, you can set the environment variables to these locations: .. prompt:: bash $ export CFLAGS="$CFLAGS -I/usr/local/include" export CXXFLAGS="$CXXFLAGS -I/usr/local/include" export LDFLAGS="$LDFLAGS -Wl,-rpath,/usr/local/lib -L/usr/local/lib -lomp" Finally, build the package using the standard command: .. prompt:: bash $ pip install --verbose --no-build-isolation --editable . For the upcoming FreeBSD 12.1 and 11.3 versions, OpenMP will be included in the base system and these steps will not be necessary. .. _OpenMP: https://en.wikipedia.org/wiki/OpenMP .. _Cython: https://cython.org .. _NumPy: https://numpy.org .. _SciPy: https://www.scipy.org .. _Homebrew: https://brew.sh .. _virtualenv: https://docs.python.org/3/tutorial/venv.html .. _conda environment: https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html .. _Miniforge3: https://github.com/conda-forge/miniforge#miniforge3 Alternative compilers ===================== The command: .. prompt:: bash $ pip install --verbose --editable . will build scikit-learn using your default C/C++ compiler. If you want to build scikit-learn with another compiler handled by ``distutils`` or by ``numpy.distutils``, use the following command: .. prompt:: bash $ python setup.py build_ext --compiler= -i build_clib --compiler= To see the list of available compilers run: .. prompt:: bash $ python setup.py build_ext --help-compiler If your compiler is not listed here, you can specify it via the ``CC`` and ``LDSHARED`` environment variables (does not work on windows): .. prompt:: bash $ CC= LDSHARED=" -shared" python setup.py build_ext -i Building with Intel C Compiler (ICC) using oneAPI on Linux ---------------------------------------------------------- Intel provides access to all of its oneAPI toolkits and packages through a public APT repository. First you need to get and install the public key of this repository: .. prompt:: bash $ wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB rm GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB Then, add the oneAPI repository to your APT repositories: .. prompt:: bash $ sudo add-apt-repository "deb https://apt.repos.intel.com/oneapi all main" sudo apt-get update Install ICC, packaged under the name ``intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic``: .. prompt:: bash $ sudo apt-get install intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic Before using ICC, you need to set up environment variables: .. prompt:: bash $ source /opt/intel/oneapi/setvars.sh Finally, you can build scikit-learn. For example on Linux x86_64: .. prompt:: bash $ python setup.py build_ext --compiler=intelem -i build_clib --compiler=intelem Parallel builds =============== It is possible to build scikit-learn compiled extensions in parallel by setting and environment variable as follows before calling the ``pip install`` or ``python setup.py build_ext`` commands:: export SKLEARN_BUILD_PARALLEL=3 pip install --verbose --no-build-isolation --editable . On a machine with 2 CPU cores, it can be beneficial to use a parallelism level of 3 to overlap IO bound tasks (reading and writing files on disk) with CPU bound tasks (actually compiling).